@opencloning/store 1.4.11 → 1.5.1

package/CHANGELOG.md

@@ -1,5 +1,13 @@
 # @opencloning/store
 
+## 1.5.1
+
+### Patch Changes
+
+- [#651](https://github.com/manulera/OpenCloning_frontend/pull/651) [`b5c89e2`](https://github.com/manulera/OpenCloning_frontend/commit/b5c89e23aa1065319cb07a9ac48a26693dd0a21a) Thanks [@manulera](https://github.com/manulera)! - Allow primer design of Gibson and similar assembly methods to include fragments that are not amplified. Similar to what the NEBuilder planner does, where not all products are amplified. Perhaps in the future it would be useful to also allow the option to restore the restriction sites on the edge.
+
+## 1.5.0
+
 ## 1.4.11
 
 ## 1.4.10

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@opencloning/store",
-  "version": "1.4.11",
+  "version": "1.5.1",
   "type": "module",
   "main": "./src/index.js",
   "exports": {

package/src/cloning.js

@@ -104,44 +104,50 @@ const reducer = {
   },
 
   addPCRsAndSubsequentSourcesForAssembly(state, action) {
-    // This is used by the PCR primer design for Gibson Assemblies. You pass a
-    // sourceId (PCR from which the primer design was started),
-    // and a list of templateIds to be amplified by PCR. Their outputs
-    // will be used as input for a subsequent assembly reaction.
+    // templateIds is the FULL ordered list of template sequence IDs.
+    // amplified[i] indicates whether templateIds[i] should go through PCR.
+    // Non-amplified templates are fed directly into the assembly.
+    // sourceId is the existing PCR source for position 0 (when amplified).
     const { sourceId, templateIds, sourceType, newSequence } = action.payload;
+    // If amplified is not provided, assume all templates are amplified
+    const amplified = action.payload.amplified || templateIds.map(() => true);
+    // Remove the current source (a PCR), in case it was not amplified,
+    // TODO: this needs to be improved in the UI, but it's like this for now.
+    state.sources = state.sources.filter((s) => s.id !== sourceId);
     const { sources, sequences } = state;
 
-    if (sources.find((s) => s.id === sourceId) === undefined) {
-      throw new Error('Source not found');
+    const pcrOutputIds = [];
+    const assemblyInputIds = [];
+
+    for (let i = 0; i < templateIds.length; i++) {
+      if (amplified[i]) {
+        const nextId = getNextUniqueId(state);
+        sources.push({
+          id: nextId,
+          input: [{ sequence: templateIds[i] }],
+          type: 'PCRSource',
+        });
+        pcrOutputIds.push(nextId);
+        assemblyInputIds.push(nextId);
+      } else {
+        assemblyInputIds.push(templateIds[i]);
+      }
     }
-    const sources2update = [sourceId];
-    // Add the PCR sources
-    templateIds.forEach((templateId) => {
-      const nextId = getNextUniqueId(state);
-      const newSource = {
-        id: nextId,
-        input: [{ sequence: templateId }],
-        type: 'PCRSource',
-      };
-      sources.push(newSource);
-      sources2update.push(newSource.id);
-    });
 
-    // Add the output sequences
-    sources2update.forEach((id) => {
-      sequences.push({
-        ...newSequence,
-        id,
-      });
+    pcrOutputIds.forEach((id) => {
+      sequences.push({ ...newSequence, id });
     });
 
     if (sourceType !== null) {
-      // Add the Assembly that takes the PCR outputs as input
-      sources.push({
+      const assemblySource = {
         id: getNextUniqueId(state),
-        input: sources2update.map((id) => ({ sequence: id })),
+        input: assemblyInputIds.map((id) => ({ sequence: id })),
         type: sourceType,
-      });
+      };
+      if (action.payload.circularAssembly !== undefined) {
+        assemblySource.circular_assembly = action.payload.circularAssembly;
+      }
+      sources.push(assemblySource);
     }
   },
 

package/src/cloning_utils.js

@@ -52,14 +52,14 @@ export function getPrimerDesignObject({ sources, sequences }) {
   const outputSequences = sequences.filter((e) => e.type === 'TemplateSequence' && Boolean(e.primer_design));
   if (outputSequences.length === 0) {
     // return 'No primer design sequence templates found';
-    return { finalSource: null, otherInputIds: [], pcrSources: [], outputSequences: [] };
+    return { finalSource: null, otherInputIds: [], pcrSources: [], outputSequences: [], assemblyInputsInOrder: [] };
   }
   const mockSequenceIds = outputSequences.map((s) => s.id);
 
   // Find the PCRs from which the mock sequences are outputs
   const pcrSources = sources.filter((s) => s.type === 'PCRSource' && mockSequenceIds.includes(s.id));
   if (pcrSources.length === 0) {
-    return { finalSource: null, otherInputIds: [], pcrSources: [], outputSequences: [] };
+    return { finalSource: null, otherInputIds: [], pcrSources: [], outputSequences: [], assemblyInputsInOrder: [] };
   }
 
   // Find the template sequences for those PCRs
@@ -68,7 +68,7 @@ export function getPrimerDesignObject({ sources, sequences }) {
   // They should not be mock sequences
   if (templateSequences.some((ts) => ts.type === 'TemplateSequence')) {
     // return 'TemplateSequence input to final source is a TemplateSequence';
-    return { finalSource: null, otherInputIds: [], pcrSources: [], outputSequences: [] };
+    return { finalSource: null, otherInputIds: [], pcrSources: [], outputSequences: [], assemblyInputsInOrder: [] };
   }
 
   // Find the source they are input to (there should be zero or one)
@@ -76,11 +76,11 @@ export function getPrimerDesignObject({ sources, sequences }) {
 
   if (finalSources.length === 0) {
     // return as is
-    return { finalSource: null, otherInputIds: [], pcrSources, outputSequences };
+    return { finalSource: null, otherInputIds: [], pcrSources, outputSequences, assemblyInputsInOrder: [] };
   }
   if (finalSources.length > 1) {
     // error
-    return { finalSource: null, otherInputIds: [], pcrSources: [], outputSequences: [] };
+    return { finalSource: null, otherInputIds: [], pcrSources: [], outputSequences: [], assemblyInputsInOrder: [] };
   }
 
   const finalSource = finalSources[0];
@@ -91,10 +91,20 @@ export function getPrimerDesignObject({ sources, sequences }) {
   // There should be no TemplateSequence as an input that does not have primer_design set
   if (otherInputs.some((i) => i.type === 'TemplateSequence' && !Boolean(i.primer_design))) {
     // return 'TemplateSequence input to final source does not have primer_design set';
-    return { finalSource: null, otherInputIds: [], pcrSources: [], outputSequences: [] };
+    return { finalSource: null, otherInputIds: [], pcrSources: [], outputSequences: [], assemblyInputsInOrder: [] };
   }
 
-  return { finalSource, otherInputIds, pcrSources, outputSequences };
+  // Build ordered assembly inputs for Gibson-like assemblies
+  const assemblyInputsInOrder = finalSource.input.map((inputItem) => {
+    const inputId = inputItem.sequence;
+    if (mockSequenceIds.includes(inputId)) {
+      const pcrSource = pcrSources.find((s) => s.id === inputId);
+      return { templateSequenceId: getPcrTemplateSequenceId(pcrSource), isAmplified: true };
+    }
+    return { templateSequenceId: inputId, isAmplified: false };
+  });
+
+  return { finalSource, otherInputIds, pcrSources, outputSequences, assemblyInputsInOrder };
 }
 
 const formatPrimer = (primer, position) => {